Precedent can absolutely be overturned, but it would be challenging to do so. Stare decisis is strongly held within the federal court system and only a very specific set of circumstances could lead to the defeat of Dover.
The most likely vector for overturning Dover would be a local attempt to promote intelligent design which was then challenged in the courts. The attempt would need to be made such that the legal challenge differed in some material way from the legal issues present in Dover. It would appeal up to a separate court of appeals, and that court would then consider Dover.
The most favorable outcome for ID proponents would be that the secondary court would issue an ambiguous or split ruling – e.g., “This case differs from Dover on points A, B, and C, but it is similar to Dover on points D and E. We concur with Dover on point D but disagree on point E.” Either party could then appeal to the SCOTUS, asking for the ambiguity to be clarified.
This whole affair would be very unlikely, though. You’d need a ridiculously partisan court to get any direct challenge to Dover past the early stages.